class: title-slide, middle, center # Fundamentals of Computational Biology ## Robert Castelo [robert.castelo@upf.edu](mailto:robert.castelo@upf.edu) ### Dept. of Experimental and Health Sciences ### Universitat Pompeu Fabra ### BSc on Human Biology ### UPF School of Health and Life Sciences ### Academic Year 2022-2023 --- class: split-four, center, font18px # Instructors .column[ <br> <br> <br>  Beatriz Calvo [MELIS-UPF](https://es.linkedin.com/in/beatrizcalvoserra) [<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#1DA1F2;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg>](https://twitter.com/beacalvo_) clinical genomics & bioinformatic methods for genomics data ] .column[ <br> <br> <br>  Robert Castelo [MELIS-UPF](https://functionalgenomics.upf.edu/people/rcastelo) [<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#1DA1F2;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg>](https://twitter.com/robertclab) statistical & bioinformatic methods for genomics data ] .column[ <br> <br> <br>  José Carlos Montañés [IMIM](https://es.linkedin.com/in/jos%C3%A9-carlos-monta%C3%B1%C3%A9s-121b30105) evolutionary genomics of de novo and duplicated genes ] .column[ <br> <br> <br>  Mireia Ramos [MELIS-UPF](https://www.upf.edu/web/endocrine-regulatory-genomics/adscripcion/-/-/185253/adscripcion/mireia-ramos) [<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:#1DA1F2;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg>](https://twitter.com/mireia_bioinfo) bioinformatic methods in molecular genetics, [@RLadiesBCN](https://twitter.com/RLadiesBCN) organizer ] --- # Computational biology * [Computational biology](https://en.wikipedia.org/wiki/Computational_biology) is the study of biology using computation. * Computational biology **is** biology, because the word _computational_ is an adjective. * Fundamentals of Computational Biology (FCB) will introduce to you concepts and basic tools of computation and information technologies, required to address biological questions using a computer. * The purpose of introducing this subject at the beginning of the curriculum is to enable the student using the tools and abilities acquired in FCB throughout the whole degree. --- # Course topics * The main topics of FCB are: &nbsp;&nbsp; * Manipulating files from the command line. * Programming and data exploration. * Development of automatized and reproducible workflows, in the context of biological data analysis. &nbsp;&nbsp; * These skills are highly and increasingly appreciated in academic and industrial environments from the life sciences. &nbsp;&nbsp; * Your CV can grow with every technique, tool or platform that you will learn to use in FCB. --- # Course structure * All sessions will be _in-person_ unless COVID19 restrictions are enforced by health authorities. In such a case we will go online-synchronous by videocall (Zoom and/or Google Meet). * There will be no _hybrid_ sessions, i.e., simultaneously _in-person_ and _online_, unless one or more students are quarantined for COVID19. * Some recorded materials from last year will be available, but part of those contents may change through this edition of the course.  --- # Course workload * One single group-class for lectures (~ 60 students/group), two for seminars (~ 30 students/group), four for practicals (~ 15 students/group) * One ECTS (~ 25hrs) throughout 10 weeks: * 3 hrs of lectures * 2 hrs of seminars * 2 hrs of practicals * 16 hrs of out-of-class work (study, assignments, etc.) * FCB has 5 ECTS, 125hrs in 10 weeks (~ 12 hr/week). Because of the learning goals of FCB, we reduce 4 hrs of lectures to have one more seminar: * **11** lectures = 11 hrs * **6** seminars x 2 hrs = 12 hrs * **10** practicals x 2 hrs = 20 hrs * 43 hrs of class time work (~ 4 hrs/week) * 82 hrs of out-of-class time work (~ 8 hrs/week) --- # Course evaluation * Continuous (60%) + final (40%) over a total of 10 points. * Continuous evaluation: * Seminars through a test on programming problem solving (1 point on the final grade): **Friday November 4th, 09:30-10:30** * Practicals through the submission of computer assignments (2 points on the final grade): ~ 8 assignments, one week submission period, penalty for late submissions. * Data analysis project (3 points on the final grade): ~ 14hrs work including 2 seminars, submission deadline ~Dec 4th, penalty for late submissions. --- # Course evaluation * Final evaluation: * Multiple-choice written exam ("PEM" in its Catalan acronym) for 50% of the final evaluation. * Open written exam ("Assaig" in Catalan) for 50% of the final evaluation. * To pass FCB at the end of the term, the student must: 1. Obtain a minimum grade of 4/10 in the average evaluation of seminars and practicals. 2. Obtain a minimum grade of 4/10 in the evaluation of the data analysis project. 3. Obtain a minimum grade of 4/10 in the final evaluation. * Remedial exam on July for the final (40%) evaluation. **It is not possible** to retake the continuous evaluation. * Even if you make a perfect July remedial exam, you won't pass FCB if you have not scratched at least 1 of the 6 points of the continuous evaluation. --- # Course evaluation * You should do the assignments **on your own**. You may ask questions on the Slack workspace, but you should not copy the assignment from a classmate. * Data analysis projects can be done individually or in teams of two people (encouraged). * The exam on programming problem solving will be **individual and in person**. * The final open written exam will be **individual and in person**. * The final multiple-choice written exam will be **individual and in person**. * You won't be able to pass FCB without sufficiently performing on the exams that you take **individually and in person**. * The best way to prepare yourself for those exams is to do the assignments on your own and work the project hand-in-hand with your mate. * Your goal shouldn't be to reach a specific mark, it should be **learning**. --- # Software tooling * You need to install in your computer the following software tools: * Unix shell: by Practical 1 on September 28th. * Text editor: by Practical 2 on October 4th. * Git version-control system: by Practical 3 on October 10th. * Python and Jupyter Notebook: by Practical 4 and October 13th. * R and RStudio Notebook: by Practical 7 on November 2nd. * You will find full instructions at https://funcompbio.github.io/setup * The first two practicals will take place in the computer room 61.303, which will be prepared with the necessary software. * The rest of the practicals (P3 starting on October 10th) will take place in a regular rooms with sockets to let you plug your laptop. * You'll need to bring your laptop with the software installed and the WiFi connection configured (see https://guiesbibtic.upf.edu/eduroam). * The library has a service that allows students to borrow a laptop. --- # Social-media productivity profiles * We will be using two social-media productivity platforms: [GitHub](https://github.com) and [Slack](https://slack.com). * You will need to create a profile in each of these platforms (instructions will follow) using your UPF student email address. * It is **very important** that you check and use your UPF student email address for any communication related to FCB. * Important announcements, deadlines, etc. related to FCB will only occur through your UPF student email address and the FCB Moodle site. * GitHub and Slack are tools to facilitate the achievement of the learning goals of FCB, but do not replace the UPF student email and FCB Moodle site for official communications. --- # Social-media productivity profiles - GitHub * **GitHub** is a provider of hosting for software development and version control using Git. * The UPF has recently become a partner school of its [education program](https://education.github.com), which will give us benefits in using [GitHub Classroom](https://classroom.github.com) for submitting and correcting assignments from practicals. * **All assignments submited through GitHub will be privately stored** under the GitHub organization repository [https://github.com/funcompbio2021](https://github.com/funcompbio2021) and **your public GitHub profile can stay completely empty**. * Your GitHub account can become a productive and powerful platform for your computational biology work: **keep it alive throughout the degree**. * You may consider using it to store some of your student assignments/projects, make them even public and make even your own professional profile; see, for instance [https://kellyjwallace.github.io](https://kellyjwallace.github.io) or [https://dieuwkehupkes.github.io](https://dieuwkehupkes.github.io), and [https://academicpages.github.io](https://academicpages.github.io) for a template to create your own personal website. --- # Social-media productivity profiles - GitHub  --- # Social-media productivity profiles - Slack * **Slack** is a messaging platform that allows one to organize messages by topic, is all searchable, facilitates sending code and attachments and integrates with other platforms, including [Google G Suite](https://gsuite.google.com/slack) and [GitHub](https://slack.github.com). * The UPF offers a Slack workspace called _upfbarcelona_ for all members of the UPF community; see [https://guiesbibtic.upf.edu/slack](https://guiesbibtic.upf.edu/slack). * We have a Slack workspace for FCB called _fcb2022upf_ associated with the URL: [https://fcb2022upf.slack.com](https://fcb2022upf.slack.com), but **it has no public profiles**.  --- # Social-media productivity profiles - Slack  --- # Moodle site * The Moodle site of FCB will be the entry point for all materials and activities.  --- # GitHub site * The GitHub site of FCB at [https://funcompbio.github.io](https://funcompbio.github.io) will store the materials (lectures, seminars and practicals), which will be linked from the Moodle site.  --- class: middle, center # Questions !?